Evaluation of the Uncertainty in Satellite-Based Crop State Variable Retrievals Due to Site and Growth Stage Specific Factors and Their Potential in Coupling with Crop Growth Models

Coupling crop growth models and remote sensing provides the potential to improve our understanding of the genotype x environment x management (G X E X M) variability of crop growth on a global scale. Unfortunately, the uncertainty in the relationship between the satellite measurements and the crop state variables across different sites and growth stages makes it diffcult to perform the coupling. In this study, we evaluate the effects of this uncertainty with MODIS data at the Mead, Nebraska Ameriflux sites (US-Ne1, US-Ne2, and US-Ne3) and accurate, collocated Hybrid-Maize (HM) simulations of leaf area index (LAI) and canopy light use effciency (LUECanopy). The simulations are used to both explore the sensitivity of the satellite-estimated genotype X management (G X M) parameters to the satellite retrieval regression coeffcients and to quantify the amount of uncertainty attributable to site and growth stage specific factors. Additional ground-truth datasets of LAI and LUECanopy are used to validate the analysis. The results show that uncertainty in the LAI/satellite measurement regression coeffcients lead to large uncertainty in the G X Mparameters retrievable from satellites. In addition to traditional leave-one-site-out regression analysis, the regression coeffcient uncertainty is assessed by evaluating the retrieval performance of the temporal change in LAI and LUECanopy. The weekly change in LAI is shown to be retrievable with a correlation coeffcient absolute value (|r|) of 0.70 and root-mean square error (RMSE) value of 0.4, which is significantly better than the performance expected if the uncertainty was caused by random error rather than secondary effects caused by site and growth stage specific factors (an expected |r| value of 0.36 and RMSE value of 1.46 assuming random error). As a result, this study highlights the importance of accounting for site and growth stage specific factors in remote sensing retrievals for future work developing methods coupling remote sensing with crop growth models

High-throughput estimation of crop traits: A review of ground and aerial phenotyping platforms

Crop yields need to be improved in a sustainable manner to meet the expected worldwide increase in population over the coming decades as well as the effects of anticipated climate change. Recently, genomics-assisted breeding has become a popular approach to food security; in this regard, the crop breeding community must better link the relationships between the phenotype and the genotype. While high-throughput genotyping is feasible at a low cost, highthroughput crop phenotyping methods and data analytical capacities need to be improved. High-throughput phenotyping offers a powerful way to assess particular phenotypes in large-scale experiments, using high-tech sensors, advanced robotics, and imageprocessing systems to monitor and quantify plants in breeding nurseries and field experiments at multiple scales. In addition, new bioinformatics platforms are able to embrace large-scale, multidimensional phenotypic datasets. Through the combined analysis of phenotyping and genotyping data, environmental responses and gene functions can now be dissected at unprecedented resolution. This will aid in finding solutions to currently limited and incremental improvements in crop yields

Improving Retrievals of Crop Vegetation Parameters from Remote Sensing Data

Agricultural systems are difficult to model because crop growth is driven by the strongly nonlinear interaction of Genotype x Environment x Management (G x E x M) factors. Due to the nonlinearity in the interaction of these factors, the amount of data necessary to develop and utilize models to accurately predict the performance of agricultural systems at an operational scale is large. Satellite remote sensing provides the potential to vastly increase the amount of data available for modelling agricultural systems as a result of its high revisit time and spatial coverage. Unfortunately, there have been significant difficulties in deploying remote sensing for many agricultural modelling applications because of the uncertainty involved in the retrievals. In this dissertation, we show that collecting farmer-provided agro-managment information has the potential to reduce the uncertainty in the retrieval products obtained from remote sensing observations. Specifically, both field-scale and regional-scale analysis are used to show that secondary factor variability is a very significant cause of uncertainty in both crop growth modelling and agricultural remote sensing that needs to be addressed through increased data collection. In order to address this need for increased data availability, a method is developed that allows geolocated crop growth model simulations to be used to train satellite-based crop state variable retrievals, which is then validated at regional scale. The method developed provides a general robust methodology to create a large-scale platform that would allow farmers to share data with government agencies and universities to improve crop state variable retrievals and crop growth modelling and provide farmers, government, industry, and researchers with insights and predictive capability into crop growth at both field and regional scales